PRS Residual Analysis - White and Black REGARDS Subjects
Jack Pattee
11/9/2023
This report documents unsupervised learning analyses of the model residuals for traits measured in white and black REGARDS subjects (documented in the ‘baseline.csv’ file downloaded from Suraju Sadeeq’s OneDrive). The following outcomes will be considered for inclusion as traits:
eGFR, documented as ‘EGFR_CKDEPI’, left ventricular hypertrophy: ‘lvh_main’, atrial fibrillation: ‘Afib_SR_ECG’, diabetes: ‘Diab_SRMed_glu’, lipidemia: ‘lipidemia_meds_labs’, myocardial infarction: ‘MI_SR_ECG’, CAD: ‘CAD_SR_ECG’, insulin, creatinine level: ‘Creatinine_urine’, albumin level: ‘Albumin_urine’, cystatin C level: ‘Cysc’, C-reactive protein: ‘Crp’, triglycerides: ‘Trigly’, glucose, LDL, HDL, DBP, SBP, cholesterol: ‘Cholest’, heart rate: ‘Heartrate’, stroke: ‘Stroke_SR’, depression (as scale): ‘CESD’.
Some variables are excluded based on inspection. CESD is highly skewed and does not appear to cohere to the Center for Epidemiological Studies - Depression scale, so it will be dropped. In this case, no subject has CESD>12, whereas the CES-D scale ranges from 0 to 60, and individuals are considered at risk for depression when the score exceeds 16.
Report the missing rate for each outcome Only one variable has missing rate >5%, which is insulin. Insulin will be dropped from consideration.
| Outcome | MissingProp |
|---|---|
| EGFR_CKDEPI | 0.025 |
| lvh_main | 0.015 |
| Diab_SRMed_glu | 0.025 |
| Lipidemia_meds_labs | 0.027 |
| Afib_SR_ECG | 0.024 |
| MI_SR_ECG | 0.018 |
| CAD_SR_ECG | 0.019 |
| insulin | 0.268 |
| Creatinine_urine | 0.047 |
| Albumin_urine | 0.049 |
| DBP | 0.003 |
| SBP | 0.003 |
| Cysc | 0.043 |
| Crp | 0.042 |
| Trigly | 0.026 |
| Glucose | 0.025 |
| Ldl | 0.041 |
| Hdl | 0.032 |
| Cholest | 0.025 |
| Heartrate | 0.012 |
| Stroke_SR | 0.003 |
The following variables will be considered as covariates in the analysis: alcohol use ‘Alc_Use’, gender ‘Gender_x’, age ‘Age_x’, smoking ‘Smoke’, education ‘ED_Cat’, income ‘Income’, weight ‘Weight’, and race ‘Race_x’.
Report the missing rate for each covariate. Income is the only covariate missing at >5%; it will be dropped, and the other seven retained. A complete case analysis will be performed on all individuals non-missing for both the covariates and the outcomes.
| Covariate | MissingProp |
|---|---|
| Weight | 0.000 |
| Smoke | 0.004 |
| Alc_Use | 0.000 |
| ED_Cat | 0.001 |
| Income | 0.123 |
| Gender_x | 0.000 |
| Race_x | 0.000 |
| Age_x | 0.000 |
PRS scores will be included as a covariate for traits where it is available. PRSs are available in white and black subjects for the following traits: eGFR (PGS000303), CAD (PGS000011), albumin (PGS000669), C-reactive protein (PGS000314), triglycerides (PGS000066), LDL (PGS000061), DBP (PGS000302), SBP (PGS000301), TC (PGS000062), and heart rate (PGS000300).
Note: the PGS for glucose (PGS000684) is present for white subjects but not black subjects.
The complete case analysis consists of 9114 subjects.
The following outcomes are binary (and thus, logistic regression will be used): LVH, Diabetes, Lipidemia, AFib, MI, CAD, Stroke. The frequency of the less common category for these binary outcomes is described below.
| Outcome | RareProp |
|---|---|
| lvh_main | 0.134 |
| Diab_SRMed_glu | 0.269 |
| Lipidemia_meds_labs | 0.448 |
| Afib_SR_ECG | 0.077 |
| MI_SR_ECG | 0.107 |
| CAD_SR_ECG | 0.144 |
| Stroke_SR | 0.059 |
Heatmap of correlation between outcome variables.
## Correlation computed with
## • Method: 'pearson'
## • Missing treated using: 'pairwise.complete.obs'
Calculate the coefficient of determination for each of the models to give a sense of how predictive each covariate is. For the logistic models, use AUROC. These plots are interpreted as follows: the point label represents the predictive accuracy of the model without that variable included.
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Assess clustering and PCs for full set of residuals.
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
Assess clustering and PCs for model residuals with each of the seven covariates held out.
## Warning: Quick-TRANSfer stage steps exceeded maximum (= 455700)## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## [1] "Adjusted rand index, no Alcohol: 0.023"
## [1] "No Alcohol table of clustering results"
## tempCovarValues
## Current Never Past
## 1 774 776 558
## 2 2895 1854 1194
## 3 422 348 293## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations## Warning: Quick-TRANSfer stage steps exceeded maximum (= 455700)## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## [1] "Adjusted rand index, no Gender: 0.013"
## [1] "No Gender table of clustering results"
## tempCovarValues
## F M
## 1 576 616
## 2 4661 3261## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations## Warning: Quick-TRANSfer stage steps exceeded maximum (= 455700)## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations## Warning: Quick-TRANSfer stage steps exceeded maximum (= 455700)## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## [1] "Adjusted rand index, no Smoking: 0.007"
## [1] "No Smoking table of clustering results"
## tempCovarValues
## Current Never Past
## 1 210 396 446
## 2 349 914 859
## 3 1014 2783 2143## Warning: did not converge in 10 iterations## Warning: Quick-TRANSfer stage steps exceeded maximum (= 455700)## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations## Warning: Quick-TRANSfer stage steps exceeded maximum (= 455700)## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## [1] "Adjusted rand index, no Education: 0.008"
## [1] "No Education table of clustering results"
## tempCovarValues
## College graduate and above High school graduate Less than high school
## 1 1347 1058 554
## 2 444 522 405
## 3 596 596 309
## 4 281 269 201
## tempCovarValues
## Some college
## 1 1162
## 2 510
## 3 589
## 4 271## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations## Warning: Quick-TRANSfer stage steps exceeded maximum (= 455700)## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations## Warning: Quick-TRANSfer stage steps exceeded maximum (= 455700)## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## Warning: did not converge in 10 iterations
## [1] "Adjusted rand index, no Race: 0.043"
## [1] "No Race table of clustering results"
## tempCovarValues
## B W
## 1 6684 1243
## 2 918 269